Mercurial > repos > iuc > snapatac2_preprocessing

annotate preprocessing.xml @ 0:b2844c6efb72 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
author iuc
date Fri, 05 Jul 2024 11:05:36 +0000
parents
children e3b85e48487b
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b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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1 <tool id="snapatac2_preprocessing" name="SnapATAC2 Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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2 <description>and integration</description>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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3 <macros>
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iuc
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4 <import>macros.xml</import>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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5 </macros>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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6 <requirements>
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7 <expand macro="requirements"/>
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8 </requirements>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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9 <command detect_errors="exit_code"><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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10 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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11 @PREP_ADATA@
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12 #end if
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13 @CMD@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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14 ]]></command>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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15 <configfiles>
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16 <configfile name="script_file"><![CDATA[
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17 @CMD_imports@
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18
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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19 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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20 @CMD_read_inputs@
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21 #end if
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22
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23 #if $method.method == 'pp.make_fragment_file'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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24 sa.pp.make_fragment_file(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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25 bam_file = '$method.bam_file',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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26 is_paired = $method.is_paired,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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27 #if $method.barcode.extract_type == 'from_tag'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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28 #if $method.barcode.barcode_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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29 barcode_tag = '$method.barcode.barcode_tag',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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30 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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31 #elif $method.barcode.extract_type == 'from_read_names'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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32 #if $method.barcode.barcode_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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33 barcode_regex = '$method.barcode.barcode_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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34 #end if
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35 #end if
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36 #if $method.umi_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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37 umi_tag = '$method.umi_tag',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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38 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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39 #if $method.umi_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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40 umi_regex = '$method.umi_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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41 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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42 shift_right = $method.shift_right,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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43 shift_left = $method.shift_left,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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44 min_mapq = $method.min_mapq,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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45 chunk_size = $method.chunk_size,
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46 compression = 'gzip',
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47 output_file = '$fragments_out',
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48 tempdir = "."
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49 )
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50
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51 #else if $method.method == 'pp.import_data'
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52 import csv
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53 with open('$method.chrom_sizes') as f:
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54 chr_sizes = {x[0]:int(x[1]) for x in csv.reader(f, delimiter='\t')}
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55
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56 sa.pp.import_data(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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57 fragment_file = '$method.fragment_file',
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58 chrom_sizes = chr_sizes,
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59 min_num_fragments = $method.min_num_fragments,
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60 sorted_by_barcode = $method.sorted_by_barcode,
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61 #if str($method.whitelist) != 'None'
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62 whitelist = '$method.whitelist',
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63 #end if
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64 shift_left = $method.shift_left,
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65 shift_right = $method.shift_right,
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66 #set $chr_mt = ([x.strip() for x in str($method.chrM).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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67 chrM = $chr_mt,
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68 chunk_size = $method.chunk_size,
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69 file = 'anndata.h5ad',
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70 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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71 )
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72
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73 #else if $method.method == 'pp.add_tile_matrix'
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74 sa.pp.add_tile_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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75 adata,
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76 bin_size = $method.bin_size,
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77 chunk_size = $method.chunk_size,
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78 #if $method.exclude_chroms != ''
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79 #set $excl_chroms = ([x.strip() for x in str($method.exclude_chroms).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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80 exclude_chroms = $excl_chroms,
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81 #end if
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82 #if $method.min_frag_size
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83 min_frag_size = $method.min_frag_size,
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84 #end if
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85 #if $method.max_frag_size
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iuc
parents:
diff changeset
86 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
87 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
88 ##counting_strategy = '$method.counting_strategy',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
89 count_frag_as_reads = $method.count_frag_as_reads,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
90 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
91 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
92
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
93 #else if $method.method == 'pp.make_gene_matrix'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
94 adata = sa.pp.make_gene_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
95 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
96 gene_anno = '$method.gene_anno',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
97 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
98 use_x = $method.use_x,
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iuc
parents:
diff changeset
99 id_type = '$method.id_type',
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iuc
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diff changeset
100 transcript_name_key = '$method.transcript_name_key',
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iuc
parents:
diff changeset
101 transcript_id_key = '$method.transcript_id_key',
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iuc
parents:
diff changeset
102 gene_name_key = '$method.gene_name_key',
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iuc
parents:
diff changeset
103 gene_id_key = '$method.gene_id_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
104 #if $method.min_frag_size
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iuc
parents:
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105 min_frag_size = $method.min_frag_size,
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iuc
parents:
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106 #end if
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iuc
parents:
diff changeset
107 #if $method.max_frag_size
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iuc
parents:
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108 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
109 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
110 ##counting_strategy = '$method.counting_strategy'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
111 count_frag_as_reads = $method.count_frag_as_reads
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iuc
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112 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
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113
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iuc
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114 #else if $method.method == 'pp.filter_cells'
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iuc
parents:
diff changeset
115 sa.pp.filter_cells(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
116 adata,
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iuc
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117 min_counts = $method.min_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
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118 min_tsse = $method.min_tsse,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
119 #if $method.max_counts
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
120 max_counts = $method.max_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
121 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
122 #if $method.max_tsse
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iuc
parents:
diff changeset
123 max_tsse = $method.max_tsse,
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iuc
parents:
diff changeset
124 #end if
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iuc
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125 inplace = True,
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iuc
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126 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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iuc
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127 )
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iuc
parents:
diff changeset
128
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iuc
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diff changeset
129 #else if $method.method == 'pp.select_features'
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iuc
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diff changeset
130 sa.pp.select_features(
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iuc
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diff changeset
131 adata,
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iuc
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132 n_features = $method.n_features,
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iuc
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133 filter_lower_quantile = $method.filter_lower_quantile,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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134 filter_upper_quantile = $method.filter_upper_quantile,
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iuc
parents:
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135 #if str($method.whitelist) != 'None'
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iuc
parents:
diff changeset
136 whitelist = '$method.whitelist',
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iuc
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diff changeset
137 #end if
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iuc
parents:
diff changeset
138 #if str($method.blacklist) != 'None'
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iuc
parents:
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139 blacklist = '$method.blacklist',
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iuc
parents:
diff changeset
140 #end if
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iuc
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diff changeset
141 max_iter = $method.max_iter,
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iuc
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142 inplace = True,
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iuc
parents:
diff changeset
143 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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iuc
parents:
diff changeset
144 )
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iuc
parents:
diff changeset
145
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iuc
parents:
diff changeset
146 #else if $method.method == 'pp.scrublet'
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iuc
parents:
diff changeset
147 sa.pp.scrublet(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
148 adata,
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iuc
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diff changeset
149 #if $method.features
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iuc
parents:
diff changeset
150 features = '$method.features',
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parents:
diff changeset
151 #end if
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iuc
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152 n_comps = $method.n_comps,
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iuc
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153 sim_doublet_ratio = $method.sim_doublet_ratio,
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iuc
parents:
diff changeset
154 expected_doublet_rate = $method.expected_doublet_rate,
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diff changeset
155 #if $method.n_neighbors
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iuc
parents:
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156 n_neighbors = $method.n_neighbors,
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parents:
diff changeset
157 #end if
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iuc
parents:
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158 use_approx_neighbors = $method.use_approx_neighbors,
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iuc
parents:
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159 random_state = $method.random_state,
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160 inplace = True,
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iuc
parents:
diff changeset
161 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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162 )
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iuc
parents:
diff changeset
163
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iuc
parents:
diff changeset
164 #else if $method.method == 'pp.filter_doublets'
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iuc
parents:
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165 sa.pp.filter_doublets(
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iuc
parents:
diff changeset
166 adata,
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iuc
parents:
diff changeset
167 #if $method.probability_threshold
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iuc
parents:
diff changeset
168 probability_threshold = $method.probability_threshold,
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parents:
diff changeset
169 #end if
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parents:
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170 #if $method.score_threshold
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iuc
parents:
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171 score_threshold = $method.score_threshold,
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iuc
parents:
diff changeset
172 #end if
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173 inplace = True,
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174 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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175 )
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176
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177 #else if $method.method == 'pp.mnc_correct'
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178 sa.pp.mnc_correct(
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179 adata,
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180 batch = '$method.batch',
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181 n_neighbors = $method.n_neighbors,
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182 n_clusters = $method.n_clusters,
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183 n_iter = $method.n_iter,
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184 @CMD_params_data_integration@
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185 inplace = True,
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186 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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187 )
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188
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189 #else if $method.method == 'pp.harmony'
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190 sa.pp.harmony(
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191 adata,
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192 batch = '$method.batch',
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193 @CMD_params_data_integration@
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194 inplace = True
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195 )
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196
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197 #else if $method.method == 'pp.scanorama_integrate'
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198 sa.pp.scanorama_integrate(
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199 adata,
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200 batch = '$method.batch',
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201 n_neighbors = $method.n_neighbors,
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202 @CMD_params_data_integration@
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203 inplace = True
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204 )
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205
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206 #else if $method.method == 'metrics.frag_size_distr'
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207 sa.metrics.frag_size_distr(
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208 adata,
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209 max_recorded_size = $method.max_recorded_size,
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210 add_key = '$method.add_key',
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211 inplace = True,
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212 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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213 )
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214
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215 #else if $method.method == 'metrics.tsse'
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216 sa.metrics.tsse(
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217 adata,
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218 gene_anno = '$method.gene_anno',
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219 inplace = True,
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220 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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221 )
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222 #end if
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223
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224 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
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225 @CMD_anndata_write_outputs@
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226 #end if
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227 ]]></configfile>
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228 </configfiles>
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229 <inputs>
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230 <conditional name="method">
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231 <param name="method" type="select" label="Method used for preprocessing">
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232 <option value="pp.make_fragment_file">Convert a BAM file to a fragment file, using 'pp.make_fragment_file'</option>
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233 <option value="pp.import_data">Import data fragment files and compute basic QC metrics, using 'pp.import_data'</option>
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234 <option value="pp.add_tile_matrix">Generate cell by bin count matrix, using 'pp.add_tile_matrix'</option>
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235 <option value="pp.make_gene_matrix">Generate cell by gene activity matrix, using 'pp.make_gene_matrix'</option>
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236 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
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237 <option value="pp.select_features">Perform feature selection, using 'pp.select_features'</option>
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238 <option value="pp.scrublet">Compute probability of being a doublet using the scrublet algorithm, using 'pp.scrublet'</option>
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239 <option value="pp.filter_doublets">Remove doublets according to the doublet probability or doublet score, using 'pp.filter_doublets'</option>
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240 <option value="pp.mnc_correct">A modified MNN-Correct algorithm based on cluster centroid, using 'pp.mnc_correct'</option>
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241 <option value="pp.harmony">Use harmonypy to integrate different experiments,using 'pp.harmony'</option>
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242 <option value="pp.scanorama_integrate">Use Scanorama [Hie19] to integrate different experiments, using 'pp.scanorama_integrate'</option>
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243 <option value="metrics.frag_size_distr">Compute the fragment size distribution of the dataset, using 'metrics.frag_size_distr'</option>
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244 <option value="metrics.tsse">Compute the TSS enrichment score (TSSe) for each cell, using 'metrics.tsse'</option>
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245 </param>
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246 <when value="pp.make_fragment_file">
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247 <param argument="bam_file" type="data" format="bam" label="File name of the BAM file"/>
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248 <param argument="is_paired" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Indicate whether the BAM file contain paired-end reads"/>
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249 <conditional name="barcode">
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250 <param name="extract_type" type="select" label="How to extract barcodes from BAM records?">
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251 <option value="from_tag">From TAG fileds</option>
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252 <option value="from_read_names">From read names using regular expressions</option>
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253 </param>
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254 <when value="from_tag">
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255 <param argument="barcode_tag" type="text" value="CB" optional="true" label="Extract barcodes from TAG fields of BAM records"/>
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256 </when>
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257 <when value="from_read_names">
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258 <param argument="barcode_regex" type="text" value="" optional="true" label="Extract barcodes from read names of BAM records using regular expressions" help="`(..:..:..:..):\w+$` extracts `bd:69:Y6:10` from `A01535:24:HW2MMDSX2:2:1359:8513:3458:bd:69:Y6:10:TGATAGGTT``"/>
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259 </when>
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260 </conditional>
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261 <param argument="umi_tag" type="text" value="" optional="true" label="Extract UMI from TAG fields of BAM records"/>
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262 <param argument="umi_regex" type="text" value="" optional="true" label="Extract UMI from read names of BAM records using regular expressions"/>
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263 <expand macro="param_shift"/>
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264 <param argument="min_mapq" type="integer" min="0" value="30" label="Filter the reads based on MAPQ"/>
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265 <expand macro="param_chunk_size" size="50000000"/>
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266 </when>
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267 <when value="pp.import_data">
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268 <param argument="fragment_file" type="data" format="interval" label="Fragment file, optionally compressed with gzip or zstd"/>
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269 <param argument="chrom_sizes" type="data" format="tabular" label="A tabular file containing chromosome names and sizes"/>
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270 <param argument="min_num_fragments" type="integer" value="200" label="Number of unique fragments threshold used to filter cells"/>
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271 <param argument="sorted_by_barcode" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether the fragment file has been sorted by cell barcodes"/>
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272 <param argument="whitelist" type="data" format="txt" optional="True" label="Whitelist file with a list of barcodes" help="Each line must contain a valid barcode. When provided, only barcodes in the whitelist will be retained."/>
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273 <param argument="chrM" type="text" value="chrM, M" label="A list of chromosome names that are considered mitochondrial DNA">
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274 <expand macro="sanitize_query"/>
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275 </param>
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276 <param argument="shift_left" type="integer" value="0" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
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277 <param argument="shift_right" type="integer" value="0" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
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278 <expand macro="param_chunk_size" size="2000"/>
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279 </when>
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280 <when value="pp.add_tile_matrix">
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281 <expand macro="inputs_anndata"/>
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282 <param argument="bin_size" type="integer" value="500" label="The size of consecutive genomic regions used to record the counts"/>
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283 <expand macro="param_chunk_size" size="500"/>
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284 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
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285 <expand macro="sanitize_query"/>
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286 </param>
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287 <expand macro="min_max_frag_size"/>
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288 <!--expand macro="param_counting_strategy"/-->
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289 <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
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290 </when>
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291 <when value="pp.make_gene_matrix">
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292 <expand macro="inputs_anndata"/>
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293 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
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294 <expand macro="param_chunk_size" size="500"/>
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295 <param argument="use_x" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, use the matrix stored in .X as raw counts"/>
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296 <param argument="id_type" type="select" label="Id type, 'gene' or 'transcript'">
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297 <option value="gene" selected="true">gene</option>
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298 <option value="transcript">transcript</option>
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299 </param>
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300 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
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301 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
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302 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
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303 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
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304 <expand macro="min_max_frag_size"/>
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305 <!--expand macro="param_counting_strategy"/-->
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306 <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
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307 </when>
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308 <when value="pp.filter_cells">
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309 <expand macro="inputs_anndata"/>
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310 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
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311 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>
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312 <param argument="max_counts" type="integer" value="" optional="true" label="Maximum number of counts required for a cell to pass filtering"/>
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313 <param argument="max_tsse" type="float" value="" optional="true" label="Maximum TSS enrichment score expressed required for a cell to pass filtering"/>
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314 </when>
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315 <when value="pp.select_features">
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316 <expand macro="inputs_anndata"/>
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317 <param argument="n_features" type="integer" min="1" value="500000" label="Number of features to keep"/>
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318 <param argument="filter_lower_quantile" type="float" min="0" value="0.005" label="Lower quantile of the feature count distribution to filter out"/>
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319 <param argument="filter_upper_quantile" type="float" min="0" value="0.005" label="Upper quantile of the feature count distribution to filter out"/>
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320 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
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321 <param argument="blacklist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide blacklist regions"/>
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322 <param argument="max_iter" type="integer" value="1" label="If greater than 1, this function will perform iterative clustering and feature selection"/>
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323 </when>
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324 <when value="pp.scrublet">
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325 <expand macro="inputs_anndata"/>
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326 <param argument="features" type="text" value="" optional="true" label=" Boolean index mask, where True means that the feature is kept, and False means the feature is removed."/>
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327 <param argument="n_comps" type="integer" value="15" label="Number of components" help="15 is usually sufficient. The algorithm is not sensitive to this parameter"/>
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328 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed cells"/>
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329 <param argument="expected_doublet_rate" type="float" value="0.1" label="Expected doublet rate"/>
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330 <param argument="n_neighbors" type="integer" value="" optional="true" label="Number of neighbors used to construct the KNN graph of observed cells and simulated doublets"/>
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331 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use approximate search"/>
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332 <param argument="random_state" type="integer" value="0" label="Random state"/>
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333 </when>
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334 <when value="pp.filter_doublets">
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335 <expand macro="inputs_anndata"/>
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336 <param argument="probability_threshold" type="float" value="0.5" label="Threshold for doublet probability"/>
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337 <param argument="score_threshold" type="float" value="" optional="true" label="Threshold for doublet score"/>
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338 </when>
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339 <when value="pp.mnc_correct">
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340 <expand macro="inputs_anndata"/>
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341 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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342 <expand macro="sanitize_query"/>
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343 </param>
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344 <param argument="n_neighbors" type="integer" value="5" label="Number of mutual nearest neighbors"/>
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345 <param argument="n_clusters" type="integer" value="40" label="Number of clusters"/>
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346 <param argument="n_iter" type="integer" value="1" label="Number of iterations"/>
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347 <expand macro="params_data_integration"/>
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348 </when>
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349 <when value="pp.harmony">
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350 <expand macro="inputs_anndata"/>
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351 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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352 <expand macro="sanitize_query"/>
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353 </param>
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354 <expand macro="params_data_integration"/>
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355 </when>
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356 <when value="pp.scanorama_integrate">
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357 <expand macro="inputs_anndata"/>
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358 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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359 <expand macro="sanitize_query"/>
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360 </param>
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361 <param argument="n_neighbors" type="integer" value="20" label="Number of mutual nearest neighbors"/>
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362 <expand macro="params_data_integration"/>
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363 </when>
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364 <when value="metrics.frag_size_distr">
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365 <!-- TODO move this to plotting -->
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366 <expand macro="inputs_anndata"/>
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367 <param argument="max_recorded_size" type="integer" min="1" value="1000" label="The maximum fragment size to record in the result"/>
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368 <param argument="add_key" type="text" value="frag_size_distr" label="Key used to store the result in `adata.uns`"/>
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369 </when>
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370 <when value="metrics.tsse">
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diff changeset
371 <!-- TODO move this to plotting -->
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372 <expand macro="inputs_anndata"/>
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373 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
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374 </when>
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375 </conditional>
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376 <expand macro="inputs_common_advanced"/>
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377 </inputs>
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diff changeset
378 <outputs>
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379 <data name="fragments_out" format="interval" label="${tool.name} (${method.method}) on ${on_string}: Fragment file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
380 <filter>method['method'] == 'pp.make_fragment_file'</filter>
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381 </data>
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382 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
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383 <filter>method['method'] != 'pp.make_fragment_file'</filter>
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diff changeset
384 </data>
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385 <data name="hidden_output" format="txt" label="Log file">
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diff changeset
386 <filter>advanced_common['show_log']</filter>
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diff changeset
387 </data>
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diff changeset
388 </outputs>
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diff changeset
389 <tests>
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390 <test expect_num_outputs="1">
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391 <!-- pp.make_fragment_file -->
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392 <conditional name="method">
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393 <param name="method" value="pp.make_fragment_file"/>
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394 <param name="bam_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21_subsample.bam"/>
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395 <param name="is_paired" value="true"/>
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396 <conditional name="barcode">
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397 <param name="extract_type" value="from_tag"/>
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398 <param name="barcode_tag" value="CB"/>
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399 </conditional>
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400 <param name="shift_left" value="4"/>
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401 <param name="shift_right" value="-5"/>
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402 <param name="min_mapq" value="10"/>
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403 <param name="chunk_size" value="50000000"/>
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404 </conditional>
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405 <output name="fragments_out" location="https://zenodo.org/records/11260316/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz" ftype="interval" compare="sim_size" delta_frac="0.1"/>
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406 </test>
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407 <test expect_num_outputs="2">
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408 <!-- pp.pp.import_data -->
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diff changeset
409 <conditional name="method">
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410 <param name="method" value="pp.import_data"/>
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411 <param name="fragment_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.tsv.gz"/>
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diff changeset
412 <param name="chrom_sizes" location="https://zenodo.org/records/11260316/files/chr21_size.tabular"/>
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413 <param name="min_num_fragments" value="1"/>
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414 <param name="sorted_by_barcode" value="False"/>
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415 <param name="shift_left" value="0"/>
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416 <param name="chrM" value="chrM, M"/>
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417 <param name="shift_right" value="0"/>
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418 <param name="chunk_size" value="1000"/>
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diff changeset
419 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
420 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
421 <param name="show_log" value="true"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
422 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
423 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
424 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
425 <has_text_matching expression="sa.pp.import_data"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
426 <has_text_matching expression="min_num_fragments = 1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
427 <has_text_matching expression="sorted_by_barcode = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
428 <has_text_matching expression="shift_left = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
429 <has_text_matching expression="chrM = \['chrM', 'M'\]"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
430 <has_text_matching expression="shift_right = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
431 <has_text_matching expression="chunk_size = 1000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
432 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
433 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
434 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
435 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
436 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
437 <!-- pp.make_gene_matrix -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
438 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
439 <param name="method" value="pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
440 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
441 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
442 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
443 <param name="use_x" value="False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
444 <param name="id_type" value="gene"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
445 <param name="transcript_name_key" value="transcript_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
446 <param name="transcript_id_key" value="transcript_id"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
447 <param name="gene_name_key" value="gene_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
448 <param name="gene_id_key" value="gene_id"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
449 <param name="count_frag_as_reads" value="True"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
450 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
451 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
452 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
453 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
454 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
455 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
456 <has_text_matching expression="sa.pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
457 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
458 <has_text_matching expression="use_x = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
459 <has_text_matching expression="id_type = 'gene'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
460 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
461 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
462 <has_text_matching expression="gene_name_key = 'gene_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
463 <has_text_matching expression="gene_id_key = 'gene_id'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
464 <has_text_matching expression="count_frag_as_reads = True"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
465 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
466 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
467 <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
468 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
469 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
470 <!-- metrics.tsse -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
471 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
472 <param name="method" value="metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
473 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
474 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
475 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
476 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
477 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
478 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
479 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
480 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
481 <has_text_matching expression="sa.metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
482 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
483 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
484 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
485 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
486 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
487 <!-- pp.filter_cells -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
488 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
489 <param name="method" value="pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
490 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
491 <param name="min_counts" value="200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
492 <param name="min_tsse" value="5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
493 <param name="max_counts" value="10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
494 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
495 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
496 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
497 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
498 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
499 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
500 <has_text_matching expression="sa.pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
501 <has_text_matching expression="min_counts = 200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
502 <has_text_matching expression="min_tsse = 5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
503 <has_text_matching expression="max_counts = 10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
504 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
505 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
506 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
507 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
508 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
509 <!-- pp.add_tile_matrix -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
510 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
511 <param name="method" value="pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
512 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
513 <param name="bin_size" value="5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
514 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
515 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
516 <param name="count_frag_as_reads" value="True"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
517 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
518 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
519 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
520 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
521 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
522 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
523 <has_text_matching expression="sa.pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
524 <has_text_matching expression="bin_size = 5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
525 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
526 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
527 <has_text_matching expression="count_frag_as_reads = True"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
528 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
529 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
530 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
531 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
532 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
533 <!-- pp.select_features -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
534 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
535 <param name="method" value="pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
536 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
537 <param name="n_features" value="15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
538 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
539 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
540 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
541 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
542 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
543 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
544 <has_text_matching expression="sa.pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
545 <has_text_matching expression="n_features = 15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
546 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
547 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
548 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
549 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
550 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
551 <!-- pp.scrublet -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
552 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
553 <param name="method" value="pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
554 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
555 <param name="n_comps" value="15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
556 <param name="sim_doublet_ratio" value="2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
557 <param name="expected_doublet_rate" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
558 <param name="random_state" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
559 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
560 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
561 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
562 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
563 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
564 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
565 <has_text_matching expression="sa.pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
566 <has_text_matching expression="n_comps = 15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
567 <has_text_matching expression="sim_doublet_ratio = 2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
568 <has_text_matching expression="expected_doublet_rate = 0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
569 <has_text_matching expression="random_state = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
570 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
571 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
572 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
573 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
574 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
575 <!-- pp.filter_doublets -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
576 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
577 <param name="method" value="pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
578 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
579 <param name="probability_threshold" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
580 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
581 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
582 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
583 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
584 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
585 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
586 <has_text_matching expression="sa.pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
587 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
588 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
589 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.filter_doublets.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
590 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
591 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
592 <!-- pp.mnc_correct -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
593 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
594 <param name="method" value="pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
595 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
596 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
597 <param name="n_neighbors" value="3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
598 <param name="n_clusters" value="10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
599 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
600 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
601 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
602 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
603 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
604 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
605 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
606 <has_text_matching expression="sa.pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
607 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
608 <has_text_matching expression="n_neighbors = 3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
609 <has_text_matching expression="n_clusters = 10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
610 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
611 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
612 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
613 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
614 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.mnc_correct.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
615 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
616 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
617 <!-- pp.harmony -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
618 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
619 <param name="method" value="pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
620 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
621 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
622 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
623 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
624 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
625 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
626 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
627 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
628 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
629 <has_text_matching expression="sa.pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
630 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
631 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
632 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
633 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
634 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.harmony.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
635 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
636 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
637 <!-- pp.scanorama_integrate -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
638 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
639 <param name="method" value="pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
640 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
641 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
642 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
643 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
644 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
645 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
646 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
647 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
648 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
649 <has_text_matching expression="sa.pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
650 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
651 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
652 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
653 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
654 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scanorama_integrate.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
655 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
656 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
657 <!-- metrics.frag_size_distr -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
658 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
659 <param name="method" value="metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
660 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
661 <param name="max_recorded_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
662 <param name="add_key" value="frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
663 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
664 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
665 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
666 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
667 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
668 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
669 <has_text_matching expression="sa.metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
670 <has_text_matching expression="add_key = 'frag_size_distr'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
671 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
672 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
673 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.frag_size_distr.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
674 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
675 </tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
676 <help><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
677 Convert a BAM file`to a fragment file, using `pp.make_fragment_file`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
678 ====================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
679
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
680 Convert a BAM file to a fragment file.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
681
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
682 Convert a BAM file to a fragment file by performing the following steps:
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
683
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
684 - Filtering: remove reads that are unmapped, not primary alignment, mapq < 30, fails platform/vendor quality checks, or optical duplicate. For paired-end sequencing, it also removes reads that are not properly aligned.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
685
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
686 - Deduplicate: Sort the reads by cell barcodes and remove duplicated reads for each unique cell barcode.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
687
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
688 - Output: Convert BAM records to fragments (if paired-end) or single-end reads.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
689
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
690 The bam file needn’t be sorted or filtered.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
691
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
692 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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693 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
694
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
695 Import data fragment file` and compute basic QC metrics, using `pp.import_data`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
696 ===============================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
697
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
698 Import data fragment files and compute basic QC metrics.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
699
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
700 A fragment refers to the sequence data originating from a distinct location in the genome. In single-ended sequencing, one read equates to a fragment. However, in paired-ended sequencing, a fragment is defined by a pair of reads. This function is designed to handle, store, and process input files with fragment data, further yielding a range of basic Quality Control (QC) metrics. These metrics include the total number of unique fragments, duplication rates, and the percentage of mitochondrial DNA detected.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
701
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
702 How fragments are stored is dependent on the sequencing approach utilized. For single-ended sequencing, fragments are found in `.obsm['fragment_single']`. In contrast, for paired-ended sequencing, they are located in `.obsm['fragment_paired']`.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
703
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
704 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
705 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_data.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
706
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
707 Generate cell by bin count matrix, using `pp.add_tile_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
708 =============================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
709
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
710 Generate cell by bin count matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
711
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
712 This function is used to generate and add a cell by bin count matrix to the AnnData object.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
713
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
714 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
715
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
716 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
717 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
718
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
719 Generate cell by gene activity matrix, using `pp.make_gene_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
720 ==================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
721
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
722 Generate cell by gene activity matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
723
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
724 Generate cell by gene activity matrix by counting the TN5 insertions in gene body regions. The result will be stored in a new file and a new AnnData object will be created.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
725
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
726 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
727
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
728 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
729 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
730
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
731 Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
732 ============================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
733
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
734 Filter cell outliers based on counts and numbers of genes expressed. For instance, only keep cells with at least `min_counts` counts or `min_ts`` TSS enrichment scores. This is to filter measurement outliers, i.e. “unreliable” observations.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
735
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
736 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
737 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_cells.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
738
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
739 Perform feature selection, using `pp.select_features`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
740 =====================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
741
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
742 Perform feature selection by selecting the most accessibile features across all cells unless `max_iter` > 1
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
743
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
744 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
745 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.select_features.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
746
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
747 Compute probability of being a doublet using the scrublet algorithm, using `pp.scrublet`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
748 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
749
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
750 Compute probability of being a doublet using the scrublet algorithm.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
751
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
752 This function identifies doublets by generating simulated doublets using randomly pairing chromatin accessibility profiles of individual cells. The simulated doublets are then embedded alongside the original cells using the spectral embedding algorithm in this package. A k-nearest-neighbor classifier is trained to distinguish between the simulated doublets and the authentic cells. This trained classifier produces a “doublet score” for each cell. The doublet scores are then converted into probabilities using a Gaussian mixture model.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
753
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
754 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
755 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scrublet.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
756
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
757 Remove doublets according to the doublet probability or doublet score, using `pp.filter_doublets`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
758 =================================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
759
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
760 Remove doublets according to the doublet probability or doublet score.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
761
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
762 The user can choose to remove doublets by either the doublet probability or the doublet score. `scrublet` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
763
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
764 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
765 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_doublets.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
766
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
767 A modified MNN-Correct algorithm based on cluster centroid, using `pp.mnc_correct`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
768 ==================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
769
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
770 A modified MNN-Correct algorithm based on cluster centroid.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
771
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
772 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
773 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.mnc_correct.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
774
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
775 Use harmonypy to integrate different experiments,using `pp.harmony`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
776 ===================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
777
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
778 Use harmonypy to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
779
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
780 Harmony is an algorithm for integrating single-cell data from multiple experiments. This function uses the python port of Harmony, `harmonypy`, to integrate single-cell data stored in an AnnData object. This function should be run after performing dimension reduction.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
781
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
782 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
783 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.harmony.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
784
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
785 Use Scanorama to integrate different experiments, using `pp.scanorama_integrate`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
786 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
787
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
788 Use Scanorama to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
789
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
790 Scanorama is an algorithm for integrating single-cell data from multiple experiments stored in an AnnData object. This function should be run after performing `tl.spectral` but before computing the neighbor graph.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
791
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
792 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
793 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scanorama_integrate.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
794
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
795 Compute the fragment size distribution of the dataset, using `metrics.frag_size_distr`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
796 ======================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
797
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
798 Compute the fragment size distribution of the dataset.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
799
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
800 This function computes the fragment size distribution of the dataset. Note that it does not operate at the single-cell level. The result is stored in a vector where each element represents the number of fragments and the index represents the fragment length. The first posision of the vector is reserved for fragments with size larger than the `max_recorded_size` parameter. `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
801
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
802 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
803 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.frag_size_distr.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
804
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
805 Compute the TSS enrichment score (TSSe) for each cell, using `metrics.tsse`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
806 ===========================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
807
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
808 Compute the TSS enrichment score (TSSe) for each cell.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
809
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
810 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
811
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
812 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
813 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.tsse.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
814
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
815 ]]></help>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
816 <expand macro="citations"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
817 </tool>